Although you can change the layout of ur base in Forces of Corruption, it's still not possible to place the power generator inside you shield... and in original EaW, you can't even place it close to the shield... why not?

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I think that on a couple maps, I've seen the enemy place their generator under the sheild. Although it only makes sense flavorwise, it would be quickly possible to make a near invincible defense... get turbolaser, concentrate all your force under the shield, *rubs hands maniacally*... darthriddick, remind me to download your mod...

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Perhaps, from a fanon/canon suspension of disbelief-type perspective, power generators are placed outside because the energies from both the annihilation of hypermatter and the ray/particle shielding would clash and cause problems. Idk, maybe it's inefficient or something.
In terms of balance it makes a degree of sense when the generator is also hidden away in a little corner of the map, certainly makes for fair opportunity. If the shield generator is easy to reach then the whole idea is a waste of time and it might as well be shielded, but if it's well defended and very hard to get to on the other hand then it's a good bit of fun for the methodical commander.

Yeah, I've seen generators inside shields. Playing EaW for the first time, Imperial campaign on Medium, attacking a Rebel planet with a shield generator inside the protective bubble. MPTL-2a armada destroyed all my forces, ended up trying to solo the entire planet with Darth Vader only.